This kind of phylogenetic tree is constructed based on differences in the genome sequence of the different species. By using different models of sequence substitution (mutations), it is possible to estimate at which point, during the course of time, the different species appeared. In addition, in order to refine this calibration of the phylogenetic tree according to time, fossil data has also been used. Fossils can easily be dated according to the deposit where they were found. By comparing the fossil species to the current ones, they can be assigned to particular branches on the phylogenetic tree and dated in this way.

Analysis of the tree shows that the origin of the Pomacentridae occured in the early Eocene and diversification continued through to the Pleistocene. The lineages of the major five subclades started to diversify between 50 and 25 million years ago. 

Based on these phylogenetic trees, statistical approaches allow the estimation of the tempo of diversification (or cladogenesis). In this study by Bruno Frédérich and colleagues, the models where the rate of cladogenesis diminishes over time did not fit with the data gathered for the Pomacentridae. The rate of diversification of this family therefore did not correspond with the unique adaptive radiation model that showed an early burst in the diversification of the species, where the tempo of the diversification was expected to slow down through time. Instead a relatively constant rate of cladogenesis can be observed. Only the genus Amphiprion, the famous clownfishes, diversified more rapidly than the other members of the family of damselfishes. This was probably due to the symbiosis it formed with sea anemones. This adaptation could therefore promote their rate of speciation.